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A graph-based multi-sample test for identifying pathways associated with cancer progression
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Cancer is in general not a result of an abnormality of a single gene but a consequence of changes in many genes, it is therefore of great importance to understand the roles of different oncogenic and tumor suppressor pathways in tumorigenesis. In recent years, there have been many computational models developed to study the genetic alterations of different pathways in the evolutionary process of cancer. However, most of the methods are knowledge-based enrichment analyses and inflexible to analyze user-defined pathways or gene sets. In this paper, we develop a nonparametric and data-driven approach to testing for the dynamic changes of pathways over the cancer progression. Our method is based on an expansion and refinement of the pathway being studied, followed by a graph-based multivariate test, which is very easy to implement in practice. The new test is applied to the rich Cancer Genome Atlas data to study the (epi)genetic alterations of 186 KEGG pathways in the development of serous ovarian cancer. To make use of the comprehensive data, we incorporate three data types in the analysis representing gene expression level, copy number and DNA methylation level. Our analysis suggests a list of nine pathways that are closely associated with serous ovarian cancer progression, including cell cycle, ERBB, JAK-STAT signaling and p53 signaling pathways. By pairwise tests, we found that most of the identified pathways contribute only to a particular transition step. For instance, the cell cycle and ERBB pathways play key roles in the early-stage transition, while the ECM receptor and apoptosis pathways contribute to the progression from stage III to stage IV. The proposed computational pipeline is powerful in detecting important pathways and gene sets that drive cancers at certain stage(s). It offers new insights into the understanding of molecular mechanism of cancer initiation and progression. © 2020 Elsevier Ltd

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Publication Date
Fri Mar 01 2024
Journal Name
Partial Differential Equations In Applied Mathematics
A hybrid technique for solving fractional delay variational problems by the shifted Legendre polynomials
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This study presents a practical method for solving fractional order delay variational problems. The fractional derivative is given in the Caputo sense. The suggested approach is based on the Laplace transform and the shifted Legendre polynomials by approximating the candidate function by the shifted Legendre series with unknown coefficients yet to be determined. The proposed method converts the fractional order delay variational problem into a set of (n + 1) algebraic equations, where the solution to the resultant equation provides us the unknown coefficients of the terminated series that have been utilized to approximate the solution to the considered variational problem. Illustrative examples are given to show that the recommended appro

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Publication Date
Wed May 15 2019
Journal Name
Al-khwarizmi Engineering Journal
Mesoporous Silica MCM-41 as a Carriers Material for Nystatine Drug in Delivery System
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In the present study, MCM-41 was synthesis as a carrier for poorly drugs soluble in water, by the sol-gel technique. Textural and chemical characterizations of MCM-41 were carried out by X-ray diffraction (XRD), Fourier transform infrared (FTIR), scanning electron microscope (SEM), and thermal gravimetric analysis (TGA). The experimental results were analyzed mesoporous carriers MCM-41. With maximum drug loading efficiency in MCM-41 determined to be 90.74%. The NYS released was prudently studied in simulated body fluid (SBF) pH 7.4 and the results proved that the release of NYS from MCM-41 was (87.79%) after 18 hr. The data of NYS released was found to be submitted a Weibull model with a correlation coefficient of (0.995). The Historical

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Publication Date
Fri Feb 15 2019
Journal Name
Journal Of Theoretical And Applied Information Technology
A system for rapid localization and intensity evaluation of saponins accumulation in plant tissues
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A fluorescence microscopy considered as a powerful imaging tool in biology and medicine. In addition to useful signal obtained from fluorescence microscopy, there are some defects in its images such as random variation in brightness, noise that caused by photon detection and some background pixels in the acquired fluorescence microscopic images appear wrongly auto-fluorescence property. All these practical limitations have a negative impact on the correct vision and analysis of the fluorescent microscope users. Our research enters the field of automation of image processing and image analysis using image processing techniques and applying this processing and analysis on one of the very important experiments in biology science. This research

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Publication Date
Tue Oct 19 2021
Journal Name
Biochem
A Neuro-Fuzzy Technique for the Modeling of β-Glucosidase Activity from Agaricus bisporus
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This paper proposes a neuro-fuzzy system to model β-glucosidase activity based on the reaction’s pH level and temperature. The developed fuzzy inference system includes two input variables (pH level and temperature) and one output (enzyme activity). The multi-input fuzzy inference system was developed in two stages: first, developing a single input-single output fuzzy inference system for each input variable (pH, temperature) separately, using the robust adaptive network-based fuzzy inference system (ANFIS) approach. The neural network learning techniques were used to tune the membership functions based on previously published experimental data for β-glucosidase. Second, each input’s optimized membership functions from the ANF

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Publication Date
Tue Jan 01 2019
Journal Name
Energy Procedia
Calculating Surface Roughness for a Large Scale SEM Images by Mean of Image Processing
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Publication Date
Sat Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance of Electro-Fenton Process for Phenol Degradation Using Nickel Foam as a Cathode
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Toxic substances have been released into water supplies in recent decades because of fast industrialization and population growth. Fenton electrochemical process has been addressed to treat wastewater which is very popular because of its high efficiency and straightforward design. One of the advanced oxidation processes (AOPs) is electro-Fenton (EF) process, and electrode material significantly affects its performance. Nickel foam was chosen as the source of electro-generated hydrogen peroxide (H2O2) due to its good characteristics. In the present study, the main goals were to explore the effects of operation parameters (FeSO4 concentration, current density, and electrolysis time) on the catalytic perform

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Publication Date
Mon Aug 01 2016
Journal Name
2016 38th Annual International Conference Of The Ieee Engineering In Medicine And Biology Society (embc)
Changes in the EEG amplitude as a biomarker for early detection of Alzheimer's disease
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The rapid increase in the number of older people with Alzheimer's disease (AD) and other forms of dementia represents one of the major challenges to the health and social care systems. Early detection of AD makes it possible for patients to access appropriate services and to benefit from new treatments and therapies, as and when they become available. The onset of AD starts many years before the clinical symptoms become clear. A biomarker that can measure the brain changes in this period would be useful for early diagnosis of AD. Potentially, the electroencephalogram (EEG) can play a valuable role in early detection of AD. Damage in the brain due to AD leads to changes in the information processing activity of the brain and the EEG which ca

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Publication Date
Wed Jan 01 2025
Journal Name
Journal Of Central European Agriculture
Power requirements for corn silage harvesters and application of precision agricultural techniques: a review
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The energy requirements of corn silage harvesters and the application of precision agricultural techniques are essential for efficient and productive agricultural practices. The article aims to review previous studies on the energy requirements needed for different corn silage harvesting machines, and on the other hand, to present methods for measuring corn silage productivity directly in the field and monitoring it based on microcontrollers and artificial intelligence techniques. The process of making corn silage is done by cutting green fodder plants into small pieces, so special harvesters are used for this, called corn silage harvesters. The purpose of harvesting corn silage is to efficiently collect and store as many digestible nutrien

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Loading and Activating a Carbon Surface and Applied for Congo Red Adsorption, Kinetic Study
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Abstract<p>this paper contains preparation of Active carbon surface (AC) from pro so millet grain husks and Loading and activating by Iron oxide and hydrogen peroxide sequentially to obtain surface (ACIPE). The changes of previous processes on Active carbon surface were diagnosed by Fourier transform infrared spectroscopy (FTIR) and Scanning electron microscopy ( SEM ). These surfaces (AC and ACIPE ) were using as adsorbent for removing of congo red dye from aqueous solutions under certain conditions through batch system. More than one kinetic model was applied to congo red dye adsorption process and it was found that the most kinetic model applied to it is a model ( pseudo second order model). </p> ... Show More
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Publication Date
Mon Jan 01 2024
Journal Name
Fifth International Conference On Applied Sciences: Icas2023
A modified Mobilenetv2 architecture for fire detection systems in open areas by deep learning
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This research describes a new model inspired by Mobilenetv2 that was trained on a very diverse dataset. The goal is to enable fire detection in open areas to replace physical sensor-based fire detectors and reduce false alarms of fires, to achieve the lowest losses in open areas via deep learning. A diverse fire dataset was created that combines images and videos from several sources. In addition, another self-made data set was taken from the farms of the holy shrine of Al-Hussainiya in the city of Karbala. After that, the model was trained with the collected dataset. The test accuracy of the fire dataset that was trained with the new model reached 98.87%.

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